JERUSALEM - Israeli police fired stun grenades and tear gas at Palestinians inside Jerusalem's Noble Sanctuary, as Prime Minister Benjamin Netanyahu called for the execution of a Palestinian who killed three Israeli settlers last week.

Clashes also broke out next to the Hutta Gate, as thousands of Muslim worshippers entered the compound, ending a boycott after Israel removed the new security measures installed after a 14 July attack left two policemen dead.

After the clashes, Israeli police were allowing people out of the Al-Aqsa site, but preventing anyone from entering.

The unrest continued into the night, as Israeli forces entered the mosque to remove protesters, according to Al-Aqsa director Omar Kiswani.

Kiswani warned of further clashes on Friday, saying Israel's crackdown on worshippers is a worrying sign.

A 12-year-old boy was injured, along with others, and several young men were arrested on Thursday night, Kiswani added.

"What happened today is intended to exact revenge on worshippers and protesters who came to pray at Al-Aqsa," he said.

Kiswani slammed the Israeli attack on protesters, calling it a violation of human norms and international law. "The world is unfortunately silent to the Israeli transgressions at Al-Aqsa."

There was also violence at Lion's Gate, the main site of protests against Israeli security measures introduced after the attack.

The Palestine Red Crescent said at least 115 people were injured in the latest violence.

Outside the compound, clashes in one area erupted when a group of policemen walked in the middle of a crowd. Palestinians threw plastic bottles and Israeli forces fired stun grenades.

Israeli police said stones were thrown at officers inside the compound.

"Upon the entry of worshippers into the Temple Mount compound, some began throwing stones at officers, during which some stones fell into the Western Wall plaza," Israeli police said in a statement, referring to the Jewish holy site below the compound.

"A police force at the site pushed back those disrupting the order using riot dispersal means. An officer was hit by a stone on his head. He was treated at the site."

The head of the Arab League warned on Thursday that Israeli attempts to control highly sensitive religious sites in Jerusalem by force risks igniting a "religious war".

Israel's actions are "playing with fire, and will only ignite a religious war and shift the core of the conflict from politics to religion," Arab League chief Ahmed Abul Gheit said.

He was speaking at a meeting of Arab foreign ministers in Cairo on the latest violence in Jerusalem.

"I invite the occupying state (Israel) to carefully learn the lessons from this crisis and the message it holds," Gheit said in a televised speech.

"Handling holy sites lightly and with this level of arrogance seriously threatens to ignite a religious war, since not one single Muslim in the world would accept the desecration of Al-Aqsa mosque," he said.

Palestinian flag removed

Videos shared on social media showed Israeli forces removing a Palestinian flag, raised hours earlier, from the entrance to the Al-Aqsa Mosque.

The fresh clashes were in stark contrast to the preceding hours, where Palestinians held street parties around the Old City after the withdrawal of Israeli police checkpoints at access points into the Noble Sanctuary, or Haram al-Sharif.

Ahmed, who was inside the mosque compound when the clashes broke out, told Middle East Eye that Israeli police had fired rubber-coated steel bullets and tear gas canisters at those who had come to pray.

"It got nasty real quick, the Israelis threw stun grenades and rubber bullets near where people were praying," said Ahmed, a British student volunteering in Palestine.

"Then they sent in the riot police and stormed the mosque compound. They then shut the gates for a while.

"People couldn't run away from the police because they're trapped inside the compound."

"Women were running and screaming to their children to avoid the rubber bullets, while the older men were telling people to calm down, and not to be afraid, that 'Al-Aqsa is ours'."

"Many people were chanting, 'We're going to Al-Aqsa'."

Speaking at a memorial service for three Israelis stabbed last week in their settlement home, Netanyahu said the death sentence should be used for "terrorists."

"The death penalty for terrorists – it's time to implement it in severe cases," he said while speaking with family members of the victims, a video of which was posted on Netanyahu's Twitter account.

"It's anchored in the law. You need the judges to rule unanimously on it, but if you want to know the government's position and my position as prime minister - in a case like this, of a base murderer like this – he should be executed. He should simply not smile anymore."